ARCHIVE: http://nyrixcorp.com/images/test.tar.gz
When rendering videos in the VSE, there are artifacts. These might just be present in HD video files- I'm not sure.
I have included an archive with a sample video and sample renders. Artifacts are particularly evident in "renders/0025.jpg". The artifacts only occur when rendering. When I use proxy/timecodes, no artifacts are present in the preview. I am using r46580 trunk of blender with the linux64 pre-compiled ffmpeg libs. I thought it might be an ffmpeg thing, but blender won't compile with the newest ffmpeg checkout, so I couldn't test it.
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This seems to be issues with file itself.
First of all you can not actually work accurate with video files without timecode. So even if you're not using proxies you'd want to use timecode to make seek accurate. Otherwise it's impossible to guarantee that seek to random frame happens correct. The only thing which might help here is doing some kind of automatic timecode which is in our todo list.
But that wouldn't help here. Seems that some frames in video are simply corrupted. You can see this even just viewing file with ffplay, so Free Run/Record Run timecodes doesn't give nice results here. If you'll use Record Run no Gaps you wouldn't have artifacts at all but your video would be shorter -- that's because frames which are failed to decode are completely ignored.
There's nothing we actually might fix here, so thanks for the report, but will close it now.